Police sealed off entrances to the church grounds after a deacon found the body of Rev. Eric Freed.
"It's a violent crime and obviously, with this kind of response, we're taking it very seriously," Chief Andrew Mills told the Times-Standard after arriving on scene.
Mills also told AP the killing occurred sometime after evening services ended on Tuesday.
CNN has more:
Local and state authorities remained at St. Bernard Church -- one of two in the coastal Northern California city situated 275 miles north of San Francisco where he was the sole pastor -- late Wednesday processing the crime scene and following up on tips, Mills said.
Those efforts include looking for Freed's vehicle, a 2010 Nissan Altima. The police chief said that authorities had no solid leads.
Calling Freed a personal friend, Mayor Frank Jager told CNN he was a "tremendous person in the community."